![]() ![]() Furthermore, they often report contigs that are not truly representative of different isoforms but arise from artifacts such as sequencing errors, repeats, variation in coverage or genetic variation within a diploid individual or pooled population. Multiple contigs, with shared sequence, arise because transcriptome assemblers differentiate between isoforms of the same gene, and report each separately. However, performing a differential expression analysis on a de novo assembled transcriptome is challenging because multiple contigs per gene are reported. One common and biologically important application of RNA-seq is identifying genes that are differentially expressed between two or more conditions. ![]() These programs are capable of assembling millions of short reads into transcript sequences - called contigs. Several programs exist for de novo transcriptome assembly: Oases and Trans-abyss, which extend the Velvet and Abyss genomic assemblers, respectively, as well as purpose built transcriptome assemblers such as Trinity. When no reference genome is available, the transcriptome is de novo assembled directly from RNA-seq reads. One of the advantages of RNA-seq over older technology, such as microarrays, is that it enables the transcriptome-wide analysis of non-model organisms because a reference genome and annotation are not required for generating and analyzing the data. Next-generation sequencing of RNA, RNA-seq, is a powerful technology for studying various aspects of the transcriptome it has a broad range of applications, including gene discovery, detection of alternative splicing events, differential expression analysis, fusion detection and identification of variants such as SNPs and post-transcriptional editing. ![]()
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